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Contents |
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* Residue conservation analysis
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Gene Ontology (GO) functional annotation
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Cellular component
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photoreceptor inner segment
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8 terms
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Biological process
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response to stimulus
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12 terms
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Biochemical function
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signal transducer activity
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6 terms
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DOI no:
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Biochemistry
40:7761-7772
(2001)
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PubMed id:
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Advances in determination of a high-resolution three-dimensional structure of rhodopsin, a model of G-protein-coupled receptors (GPCRs).
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D.C.Teller,
T.Okada,
C.A.Behnke,
K.Palczewski,
R.E.Stenkamp.
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ABSTRACT
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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J.Labrecque,
M.Metz,
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HIV-1 entry inhibition by small-molecule CCR5 antagonists: A combined molecular modeling and mutant study using a high-throughput assay.
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Virology, 413,
231-243.
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K.J.Gregory,
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Allosteric modulation of metabotropic glutamate receptors: structural insights and therapeutic potential.
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Neuropharmacology, 60,
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The opsin shift and mechanism of spectral tuning in rhodopsin.
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J Comput Chem, 32,
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Color tuning in short wavelength-sensitive human and mouse visual pigments: ab initio quantum mechanics/molecular mechanics studies.
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J Phys Chem A, 113,
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Topology of class A G protein-coupled receptors: insights gained from crystal structures of rhodopsins, adrenergic and adenosine receptors.
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Mol Pharmacol, 75,
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D.T.Lodowski,
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Comparative Analysis of GPCR Crystal Structures.
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Photochem Photobiol, 85,
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G.Khelashvili,
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M.C.Pitman,
and
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(2009).
Structural and dynamic effects of cholesterol at preferred sites of interaction with rhodopsin identified from microsecond length molecular dynamics simulations.
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Proteins, 76,
403-417.
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G.Li,
K.M.Haney,
G.E.Kellogg,
and
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(2009).
Comparative docking study of anibamine as the first natural product CCR5 antagonist in CCR5 homology models.
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J Chem Inf Model, 49,
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G.Li,
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14-O-Heterocyclic-substituted naltrexone derivatives as non-peptide mu opioid receptor selective antagonists: design, synthesis, and biological studies.
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Bioorg Med Chem Lett, 19,
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R.B.Westkaemper,
and
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(2009).
Design, synthesis, and biological evaluation of 6alpha- and 6beta-N-heterocyclic substituted naltrexamine derivatives as mu opioid receptor selective antagonists.
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J Med Chem, 52,
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J.C.Mobarec,
R.Sanchez,
and
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(2009).
Modern homology modeling of G-protein coupled receptors: which structural template to use?
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J Med Chem, 52,
5207-5216.
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J.Devillé,
J.Rey,
and
M.Chabbert
(2009).
An indel in transmembrane helix 2 helps to trace the molecular evolution of class A G-protein-coupled receptors.
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J Mol Evol, 68,
475-489.
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J.Lättig,
A.Oksche,
M.Beyermann,
W.Rosenthal,
and
G.Krause
(2009).
Structural determinants for selective recognition of peptide ligands for endothelin receptor subtypes ETA and ETB.
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J Pept Sci, 15,
479-491.
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J.M.Klco,
S.Sen,
J.L.Hansen,
C.Lyngsø,
G.V.Nikiforovich,
S.P.Sheikh,
and
T.J.Baranski
(2009).
Complement factor 5a receptor chimeras reveal the importance of lipid-facing residues in transport competence.
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FEBS J, 276,
2786-2800.
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M.Aguilà,
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M.Morillo,
M.Dominguez,
B.Vaz,
R.Alvarez,
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and
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(2009).
Structural Coupling of 11-cis-7-Methyl-retinal and Amino Acids at the Ligand Binding Pocket of Rhodopsin.
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Photochem Photobiol, 85,
485-493.
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M.F.Brown,
K.Martínez-Mayorga,
K.Nakanishi,
G.F.Salgado,
and
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(2009).
Retinal Conformation and Dynamics in Activation of Rhodopsin Illuminated by Solid-state H NMR Spectroscopy.
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Photochem Photobiol, 85,
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M.Möller,
and
U.Alexiev
(2009).
Surface Charge Changes upon Formation of the Signaling State in Visual Rhodopsin.
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Photochem Photobiol, 85,
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P.A.Boucher,
C.E.Morris,
and
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Mechanosensitive closed-closed transitions in large membrane proteins: osmoprotection and tension damping.
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Biophys J, 97,
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S.Ananthan,
W.Zhang,
and
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Recent advances in structure-based virtual screening of G-protein coupled receptors.
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AAPS J, 11,
178-185.
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S.Costanzi,
J.Siegel,
I.G.Tikhonova,
and
K.A.Jacobson
(2009).
Rhodopsin and the others: a historical perspective on structural studies of G protein-coupled receptors.
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| |
Curr Pharm Des, 15,
3994-4002.
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S.Gleim,
A.Stojanovic,
E.Arehart,
D.Byington,
and
J.Hwa
(2009).
Conserved rhodopsin intradiscal structural motifs mediate stabilization: effects of zinc.
|
| |
Biochemistry, 48,
1793-1800.
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T.E.Angel,
M.R.Chance,
and
K.Palczewski
(2009).
Conserved waters mediate structural and functional activation of family A (rhodopsin-like) G protein-coupled receptors.
|
| |
Proc Natl Acad Sci U S A, 106,
8555-8560.
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T.E.Angel,
S.Gupta,
B.Jastrzebska,
K.Palczewski,
and
M.R.Chance
(2009).
Structural waters define a functional channel mediating activation of the GPCR, rhodopsin.
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Proc Natl Acad Sci U S A, 106,
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X.J.Yao,
G.Vélez Ruiz,
M.R.Whorton,
S.G.Rasmussen,
B.T.DeVree,
X.Deupi,
R.K.Sunahara,
and
B.Kobilka
(2009).
The effect of ligand efficacy on the formation and stability of a GPCR-G protein complex.
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Proc Natl Acad Sci U S A, 106,
9501-9506.
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A.Altun,
S.Yokoyama,
and
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(2008).
Spectral tuning in visual pigments: an ONIOM(QM:MM) study on bovine rhodopsin and its mutants.
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J Phys Chem B, 112,
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A.L.Parrill
(2008).
Lysophospholipid interactions with protein targets.
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Biochim Biophys Acta, 1781,
540-546.
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A.Martinelli,
and
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(2008).
Molecular modeling of adenosine receptors: new results and trends.
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Med Res Rev, 28,
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N.Ferré,
and
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(2008).
An artificial molecular switch that mimics the visual pigment and completes its photocycle in picoseconds.
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Proc Natl Acad Sci U S A, 105,
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and
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High-resolution distance mapping in rhodopsin reveals the pattern of helix movement due to activation.
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Proc Natl Acad Sci U S A, 105,
7439-7444.
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D.J.Müller,
N.Wu,
and
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(2008).
Vertebrate membrane proteins: structure, function, and insights from biophysical approaches.
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Pharmacol Rev, 60,
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D.Marsh
(2008).
Energetics of hydrophobic matching in lipid-protein interactions.
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Biophys J, 94,
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(2008).
Active state-like conformational elements in the beta2-AR and a photoactivated intermediate of rhodopsin identified by dynamic properties of GPCRs.
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Biochemistry, 47,
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Atomistic insights into rhodopsin activation from a dynamic model.
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J Am Chem Soc, 130,
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(2008).
Advances in the Development and Application of Computational Methodologies for Structural Modeling of G-Protein Coupled Receptors.
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Expert Opin Drug Discov, 3,
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J.H.Kim,
E.Y.Cho,
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Characterization of functional roles of DRY motif in the 2nd intracellular loop of dopamine D2 and D3 receptors.
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Arch Pharm Res, 31,
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M.S.Taylor,
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(2008).
Mutations affecting the oligomerization interface of G-protein-coupled receptors revealed by a novel de novo protein design framework.
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Biophys J, 94,
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P.S.Park,
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Activation of g protein-coupled receptors: beyond two-state models and tertiary conformational changes.
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Annu Rev Pharmacol Toxicol, 48,
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Terahertz spectroscopy of bacteriorhodopsin and rhodopsin: similarities and differences.
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Biophys J, 94,
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Structural insights into G-protein-coupled receptor activation.
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Curr Opin Struct Biol, 18,
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W.M.Oldham,
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Nat Rev Mol Cell Biol, 9,
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J Comput Chem, 28,
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Proteins, 67,
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B.K.Kobilka
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G protein coupled receptor structure and activation.
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Biochim Biophys Acta, 1768,
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K.Chen,
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(2007).
Understanding the regulation mechanisms of PAF receptor by agonists and antagonists: molecular modeling and molecular dynamics simulation studies.
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Proteins, 67,
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PDB code:
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|
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C.M.Taylor,
G.V.Nikiforovich,
and
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(2007).
Defining the interface between the C-terminal fragment of alpha-transducin and photoactivated rhodopsin.
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Biophys J, 92,
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D.Marsh
(2007).
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Biophys J, 93,
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D.T.Lodowski,
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J.A.Ballesteros,
K.Palczewski,
and
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(2007).
Crystal packing analysis of Rhodopsin crystals.
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| |
J Struct Biol, 158,
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L.Bosch,
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and
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(2007).
Critical role of electrostatic interactions of amino acids at the cytoplasmic region of helices 3 and 6 in rhodopsin conformational properties and activation.
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J Biol Chem, 282,
14272-14282.
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F.Lumento,
V.Zanirato,
S.Fusi,
E.Busi,
L.Latterini,
F.Elisei,
A.Sinicropi,
T.Andruniów,
N.Ferré,
R.Basosi,
and
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(2007).
Quantum chemical modeling and preparation of a biomimetic photochemical switch.
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Angew Chem Int Ed Engl, 46,
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J.D.Otero-Cruz,
C.A.Báez-Pagán,
I.M.Caraballo-González,
and
J.A.Lasalde-Dominicci
(2007).
Tryptophan-scanning mutagenesis in the alphaM3 transmembrane domain of the muscle-type acetylcholine receptor. A spring model revealed.
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J Biol Chem, 282,
9162-9171.
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J.M.Laurila,
H.Xhaard,
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M.J.Rantanen,
H.K.Karlsson,
M.S.Johnson,
and
M.Scheinin
(2007).
The second extracellular loop of alpha2A-adrenoceptors contributes to the binding of yohimbine analogues.
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Br J Pharmacol, 151,
1293-1304.
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J.Stitham,
E.Arehart,
S.R.Gleim,
N.Li,
K.Douville,
and
J.Hwa
(2007).
New insights into human prostacyclin receptor structure and function through natural and synthetic mutations of transmembrane charged residues.
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| |
Br J Pharmacol, 152,
513-522.
|
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|
K.D.Ridge,
and
K.Palczewski
(2007).
Visual rhodopsin sees the light: structure and mechanism of G protein signaling.
|
| |
J Biol Chem, 282,
9297-9301.
|
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|
K.h.T.Kholmurodov,
T.B.Fel'dman,
and
M.A.Ostrovskii
(2007).
Molecular dynamics of rhodopsin and free opsin: computer simulation.
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| |
Neurosci Behav Physiol, 37,
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L.A.Montero-Cabrera,
U.Röhrig,
J.A.Padrón-Garcia,
R.Crespo-Otero,
A.L.Montero-Alejo,
J.M.Garcia de la Vega,
M.Chergui,
and
U.Rothlisberger
(2007).
CNDOL: A fast and reliable method for the calculation of electronic properties of very large systems. Applications to retinal binding pocket in rhodopsin and gas phase porphine.
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| |
J Chem Phys, 127,
145102.
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L.M.Frutos,
T.Andruniów,
F.Santoro,
N.Ferré,
and
M.Olivucci
(2007).
Tracking the excited-state time evolution of the visual pigment with multiconfigurational quantum chemistry.
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Proc Natl Acad Sci U S A, 104,
7764-7769.
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M.L.Matsumoto,
K.Narzinski,
P.D.Kiser,
G.V.Nikiforovich,
and
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(2007).
A comprehensive structure-function map of the intracellular surface of the human C5a receptor. I. Identification of critical residues.
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J Biol Chem, 282,
3105-3121.
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P.S.Crozier,
M.J.Stevens,
and
T.B.Woolf
(2007).
How a small change in retinal leads to G-protein activation: initial events suggested by molecular dynamics calculations.
|
| |
Proteins, 66,
559-574.
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N.Berova,
and
K.Nakanishi
(2001).
On the bioactive conformation of the rhodopsin chromophore: absolute sense of twist around the 6-s-cis bond.
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Chemistry, 7,
4198-4204.
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